Targeted Sequencing using NGS platforms
MarkerMiner is an easy-to-use, fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. It first identifies clusters of single-copy gene transcripts present in each user-provided transcriptome assembly. Each single-copy gene cluster is run through a multiple sequence alignment and it outputs MSA files that can be used to assess phylogenetic utility or, if appropriate, to conduct preliminary phylogenetic analyses. Lastly, each of the single-copy gene MSAs are re-aligned with MAFFT profile alignment step using a user-selected coding reference sequence with intronic regions represented as Ns. Users can use MarkerMiner’s profile alignment output to identify putative splice junctions in the transcripts and to design primers or probes for targeted sequencing.
Pipeline Analysis for Next Generation Amplicons
High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze, and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching, and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities.
Alternative splicing analysis with RNA-Seq
PASTA is a software pipeline for the analysis of RNA-Sequencing data. It provides an innovative algorithm for the accurate, unbiased identification of splice junctions; automatic generation of gene models from junction information, both annotation-based or de novo; and estimation of relative expression changes of individual exons and junctions or entire isoforms.
Computational Detection of Transcription Factor Binding Sites
MAPPER is an integrated platform for the computational analysis of Transcription Factor Binding Sites (TFBS) in multiple genomes. It includes a library of over 1,000 TFBS models, a database of predicted binding sites in the promoters of all human, mouse and Drosophila genes, a search engine to scan user-provided sequences in real time, and rSNPs-MAPPER, a tool to predict the effect of Single Nucleotide Polymorphysms on TFBSs. Other MAPPER features include: a tool to create new TFBS models from binding site alignments, extensive data annotation and export capabilities, and a powerful, user-friendly interface.
The Tree of Life Knowledge and Information Network
TOLKIN is an information management and analytical web application to provide informatics support for phylodiversity and biodiversity research projects. As a web-based application, TOLKIN is able to support collaborative projects by providing shared access to a variety of data on voucher specimens, taxonomy, bibliography, morphology, DNA samples and sequences.